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He was second son of Gawen Hamilton, third son of Hans Hamilton, vicar of Dunlop. After receiving a liberal education at Glasgow he was appointed by his uncle, James Hamilton, 1st Viscount Claneboye, overseer and general manager of his estates in Ireland. He attracted the attention of Robert Blair, at that time minister of the church at Bangor, County Down, who persuaded him to enter the ministry. In 1626, despite heterodox views which resembled Blair's own in regard to episcopacy, he was ordained by Bishop Robert Echlin, and presented by Lord Claneboye to the church at Ballywalter in co. Down.

He was there for ten years until Thomas Wentworth and John Bramhall set new terms of church communion to be sworn to in the Church of Ireland. Hamilton did not submit, and his example was followed by other ministers including Edward Brice and John Ridge.[1][2]Henry Leslie, Echlin's successor, was urged by Bramhall to proceed to their deposition; Leslie challenged them to a public disputation. His challenge was accepted, and Hamilton was chosen to conduct the defence on their behalf. The conference opened on 11 August 1636, in the presence of a large assembly. Bramhall called a halt, and, having obtained an adjournment, persuaded Leslie not to resume it, but to pass sentence on the recalcitrant ministers. On the following day they were deposed. Warrants were issued for their arrest, and Hamilton left for Scotland, where he was appointed minister of the church at Dumfries.

In September 1642 he revisited Ireland, in order to minister to the Ulster Scots, but returning to Scotland he was in March 1644 appointed by the general assembly to superintend the administration of the solemn league and covenant in Ulster. On his return to Scotland the ship in which he and several others, including his father-in-law, had taken their passage, was captured by the "Harp", a Wexford frigate, commanded by Alaster MacDonnell, who was bringing reinforcements to James Graham, 1st Marquess of Montrose in the Highlands. MacDonnell, who hoped by an exchange of prisoners to secure the release of his father, Colkittagh, then in the hands of Archibald Campbell, 1st Marquess of Argyll, landed his prisoners at Ardnamurchan, and confined them in Mingary Castle. There Hamilton remained for ten months; several of his companions were released, but his father-in-law, the Rev. David Watson, and another minister, Mr. Weir, both died. Exertions of the general assembly and Scottish parliament set him free on 2 May 1645.

By his wife, Elizabeth Watson, daughter of David Watson, minister of Killeavy, near Newry, he had fifteen children, all of whom died in their infancy except one son, Archibald, who was a leading minister in the presbyterian church in Ireland, and three daughters, Jane, Mary, and Elizabeth.